Dark valence electrons and color vision

By its large orbital radius dark valence electron (dark in TGD sense, h_eff=n× h) sees atomic nucleus and other electrons, which are ordinary, effectively as an object of charge Z_eff=1. Dark valence electron has reduced mass which in excellent approximation equals to that of electron so that the spectrum of bound state energies and transition energies is scaled down by the factor (h/h_eff)². This irrespective of what the atom is. The only condition is that there is single unpaired valence electron guaranteed if Z for the atom is odd. For even Z an odd number of valence electrons must be associated with valence bonds: this would be the case for OH radical for instance.

The dynamics of dark valence electrons is universal with universal transition energy spectrum. One obtains a fractal hierarchy of dynamics labelled by the value of (h/h_eff)², where h_eff=n× h₀, h₀ the minimal value of Planck constant, not necessary equal to h so that one has h=n₀× h₀. The quantum critical dynamics characterizing living matter in TGD Universe is indeed universal.

The dark photon communications in living matter could utilize these universal energy spectra besides cyclotron energy spectrum and Larmor spectrum assignable to dark particles at flux tubes and the spectrum of generalized Josephson frequencies assignable to cell membrane. In particular, vision and even other sensory modalities could rely on the transitions induced by the absorption of dark valence electron. In TGD also other sensory percepts are communicated from sensory receptors to the sensory areas of cortex (see this) and also here same universal transition energies of dark valence electrons might be involved.

This hypothesis when combined with the earlier ideas about color qualia leads to a highly predictive and testable model for the perception of colors. In particular the condition h=n₀× h₀, n₀>1, is necessary for the model to work. n₀=4 and n₀=6 look the most realistic options. For n₀=4 the number of values of n=8,9,10 and correspond to the number 3 of color sensitive receptors whereas n₀=6 the number of values n=12,13,14,15 suggests the existence of a fourth color receptor sensitive to red light.

The statistical aspects of color summation can be understood from TGD inspired theory of consciousness in terms of the hypothesis that self experiences the mental images of sub-self as kind of statistical averages. The identification of quark colors as fundamental color qualia, the entanglement of quarks and antiquarks to form states in one-one correspondence with charged gluons, and the twistor space of CP₂ play key roles in the model of color summation.

Remark: There is experimental evidence for the notion of dark valence electron coming from the decades old anomaly related to rare Earth metals (see this). For TGD based model see this). This finding led to a proposal that valence bonds could also involve non-standard values of Planck constant (see this).

See the article Dark valence electrons and color vision or chapter of "TGD based view about living matter and remote mental interactions" with the same title.

Does RNA code for pain?

Again an extremely interesting finding from neuroscience. The popular article "Scientists Sucked a Memory Out of a Snail and Stuck It in Another Snail" tells that the conditionings of snails produced by painful sensations can be transferred to other snails or even snail neurons in Petri dish by adding just the RNA of the conditioned snails to the dish! The article can be found at here .

Let us summarize the findings.

1. RNA from snails is transferred to snails or to even populations of snail neurons in Petri dish!
   
   
2. The effect involves epigenetic changes in DNA by methylation induced by RNA somehow. The reaction is to the serotonin informing for the stimulus. Avoidance behavior emerges as a response.
   
   
3. How does RNA induce the epigenetic change? RNA should couple to a a specific part of DNA and induce the effect. A pairing of DNA with RNA in question occurring also in transcription suggests itself strongly.
   
   
4. What in the RNA of the conditioned snail is different? RNA should somehow code for the conditioning induced by a painful sensory experience. RNA of sensory receptors should change somehow and communicate this change to DNA in brain by some mechanism. DNA-RNA pairing does not seem plausible. Could the pairing occur by some other means?
   
   

Before continuing it is good to summarize the TGD based models for music harmony providing also a model of genetic code (see this), for sensory perception (see this), for emotions (see this), and for impriting of emotions in water (see this).

1. TGD based model for emotions and communication of emotions suggests that the communication takes place in terms of what I call music of light (also sound might be involved). Music expresses and creates emotions. Emotional state, mood, is coded by harmony or disharmony for music of light.
   

   12-note is fundamental for music and is represented as a closed self-non-intersecting path (Hamilton cycle) at icosahedron having 12 vertices. Icosahedron has 20 faces (triangles) and for given Hamilton cycle one can assign a 3-chord to each triangle. This gives 20-chord harmony (or disharmony). There is quite large number of 20-chord harmonies and those allowing Z₆,Z₄ and Z₂ as symmetries is quite large. Besides this there 6 cycles with no symmetries and these could be identified as dis-harmonies.
   
   

2. 20 is also the number of amino-acids so that it is not totally surprising that the model for bioharmony as a union of 3 different 20-chord harmonies plus 4-chord harmony assignable to tetrarhedron turns out to give a model of genetic code as 64 chord bioharmony. There are 64 basic 3-chords in one-one correspondence with DNA and RNA codons. tRNA corresponds to a union of 2 20-chord harmonies. Given amino-acid corresponds to the orbit of 3-chord under symmetries of the harmony so that number of 3-chords at the orbit is the number of DNAs coding for the amino-acid. These numbers come out correctly.
   
   
3. There are two other representations of genetic code. The ordinary chemical representation and the representation in terms of dark proton sequences at magnetic flux tubes. The model for dark proton triplet predicts that its states divided to 64 analogs of DNA codons, 64 analogs of RNA codons, 40 analogs of tRNA codons, and 20 analogs of amino-acids. Genetic code comes out correctly also now by a natural pairing of dark proton triplets. One must couple these 3 representations of genetic code with themselves and with each other.
   
   
4. There is indeed resonant coupling by 3-chords realized in terms of free frequencies of dark photons. The frequencies are rather low (E =h_eff× f, h_eff/h=n) but energies are same as for biophotons with energies in visible and UV range.
   

   Also dark variants of DNA, etc couple with each other via dark photon resonance. Dark DNA,etc couple with ordinary DNA, etc.. by energy resonance to form double strands. This means that dark photon transforms to ordinary photon in the coupling. Amino-acid couples to single frequency, which is the sum of codon frequencies coding for it.
   

   There is quite large number of 3-chord 3-harmonies defining DNA and RNA moods, and 3-chord 2-harmonies tRNA moods, and amino-acid 1-chord harmonies. There also 6 disharmonies with 20 chords each possible assignable to negative moods such as those generated by pain.
   
   

So: Is the communication chemical by DNA-RNA pairing or by some other means? TGD based model suggests "some other means".

1. Pain in sensory receptor is certainly involved. In TGD based model differs from neuroscience view in that for sensory experiences sensory receptors are seats of the sensory qualia and brain only forms cognitive representations about them and also entangles with sensory receptors to share the pain. Somehow pain must affect RNA in sensory receptors? How?
   
   
2. In this framework the stimulus in nocireceptors would induce a disharmony expressed in terms of the disharmony associated with the expression of RNA in terms of 3-chords. The dark variant of RNA in pain receptors would entangle with the dark DNA in certain neurons in brain of the snail. Nerve pulse patterns from the nociceptors would generate also magnetic flux tube connections parallel to the sensory pathway in question and make possible the communication by dark biophoton triplets to brain possible. The dark variant of DNA in brain would have resonant coupling with ordinary DNA and induce the epigenetic change by methylation as a response to the negative mood with the mediary of biophotons. After this the organism would have avoidance behaviour towards the stimulus inducing the pain.
   
   
3. The presence of mere RNA and associated dark RNA dis-harmonious mood would do the same for any neuron by the resonance mechanism. This would allow to transfer emotions even to snail neurons in Petri dish, not only those in living snails.
   

The proposed mechanism provides insights to many other poorly understood problems.

1. This mechanism also allows to understand how the transfer of emotions conditioning induces epigenetic chance also in the germ cell DNA: this is not easy to understand in the standard framework requiring chemical communication through the germ cell membrane.
   
   
2. The models for learning (memories restricted to conditionings) based on formation of synaptic contacts on one hand and involving RNA are seen as exclusive in standard neuroscience. In TGD framework the formation of synaptic contacts might rely at the fundamental level on the same epigenetic mechanism. Neuromodulators might induce the emotional states in RNA in turn doing the epigenetic editing.
   

   In human brain the genomes differ in various neurons and epigenetic editing by the proposed mechanism might cause this. An interesting question is whether humans could edit their genomes intentionally. All conditionings are not useful and maybe it becomes someday possible to affect these conditionings at the level of dark DNA.
   
   

3. Squid and octopus are known to be able to edit their mRNA (see this). Instead of DNA the mRNA produced in the transcription so that the translation produce different protein. The effect of emotional states of the dark variant of RNA associated with mRNA could be the mechanism involved.
   
   
4. The strong emotional state of single individual induces very effectively the same emotional state in people around: consider only concert as an example. Could the "music of dark light" mediate the emotions from the dark RNA of individual - say artist - to people around. If so all art would be basically music of light!
   
   

To sum up: this finding provides rather concrete support for the vision that emotions are coded by the music of light at molecular level.

See the article Emotions as sensory percepts about the state of magnetic body? or the chapter of "TGD based view about living matter and remote mental interactions" with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

The experiments of Masaru Emoto with emotional imprinting of water

Sini Kunnas sent a link to a video telling about experiments of Masaru Emoto (see this) with water, which is at criticality with respect to freezing and then frozen. Emoto reports is that words expressing emotions are transmitted to water: positive emotions tend to generate beautiful crystal structures and negative emotions ugly ones. Also music and even pictures are claimed to have similar effects. Emoto has also carried out similar experiments with rice in water. Rice subjected to words began to ferment and water subject to words expressing negative emotions began to rotten.

Remark: Fermentation is a metabolic process consuming sugar in absence of oxygen. Metabolism is a basic signature of life so that at least in this aspect the water+rice system would become alive. The words expressing positive emotions or even music would serve as a signal "waking up" the system.

One could define genuine skeptic as a person who challenges existing beliefs and pseudo-skeptic (PS in the sequel) as a person challenging - usually denying - everything challenging the mainstream beliefs. The reception of the claims of Emoto is a representative example about the extremely hostile reactions of PSs as aggressive watchdogs of materialistic science towards anything that challenges their belief system. The psychology behind this attitude is same as behind religious and political fanatism.

I must emphasize that I see myself as a thinker and regard myself as a skeptic in the old-fashioned sense of the word challenging the prevailing world view rather than phenomena challenging the prevailing world view. I do not want to be classified as believer or non-believer. The fact is that if TGD inspired theory of consciousness and quantum biology describes reality, a revolution in the world view is unavoidable. Therefore it is natural to consider the working hypothesis that the effects are real and see what the TGD based explanation for them could be.

The Wikipedia article about Masaru Emoto (see this) provides a good summary of the experiments of Emoto and provides a lot of links so that I will give here only a brief sketch. According to the article Emoto believed that water was a "blueprint for our reality" and that emotional "energies" and "vibrations" could change the physical structure of water. The water crystallization experiments of Emoto consisted of exposing water in glasses to different words, pictures or music, and then freezing and examining the aesthetic properties of the resulting crystals with microscopic photography. Emoto made the claim that water exposed to positive speech and thoughts would result in visually "pleasing" crystals being formed when that water was frozen, and that negative intention would yield "ugly" crystal formations.

In 2008, Emoto and collaborators published and article titled "Double-Blind Test of the Effects of Distant Intention on Water Crystal Formation" about his about experiments with water in the Journal of Scientific Exploration, a peer reviewed scientific journal of the Society for Scientific Explorations (see this). The work was performed by Masaru Emoto and Takashige Kizu of Emoto’s own IHM General Institute, along with Dean Radin and Nancy Lund of the Institute of Noetic Sciences, which is on Stephen Barrett's Quackwatch (see this) blacklist of questionable organizations. PSs are the modern jesuits and for jesuits the end justifies the means.

Emoto has also carried experiments with rice samples in water. There are 3 samples. First sample "hears" words with positive emotional meaning, second sample words with negative emotional meaning, and the third sample serving as a control sample. Emoto reports (see this) that the rice subjected to words with positive emotional content began to ferment whereas water subject to words expressing negative emotions began to rotten. The control sample also began to rotten but not so fast.

In the article The experiments of Masaru Emoto with emotional imprinting of water I will consider the working hypothesis that the effects are real, and develop an explanation based on TGD inspired quantum biology. The basic ingredients of the model are following: magnetic body (MB) carrying dark matter as h_eff/h=n phases of ordinary matter; communications between MB and biological body (BB) using dark photons able to transform to ordinary photons identifiable as bio-photons; the special properties of water explained in TGD framework by assuming dark component of water implying that criticality for freezing involves also quantum criticality, and the realization of genetic code and counterparts of the basic bio-molecules as dark proton sequences and as 3-chords consisting of light or sound providing a universal language allowing universal manner to express emotions in terms of bio-harmony realized as music of light or sound. The entanglement of water sample and the subject person (with MBs included) realized as flux tube connections would give rise to a larger conscious entity expressing emotions via language realized in terms of basic biomolecules in a universal manner by utilizing genetic code realized in terms of both dark proton sequences and music of light of light and sound.

See the article The experiments of Masaru Emoto with emotional imprinting of water or the chapter Dark Nuclear Physics and Condensed Matter of "Hyper-finite factors, p-adic length scale hypothesis, and dark matter hierarchy".

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Homonymy of the genetic code from TGD point of view

The article behind the following considerations was motivated by the article of Peter Gariaev about the linguistic notions of synonymy and homonymy applied to genetic code. Homonymy is visible in mRNa-tRNA pairing and induced by the 1-to-many pairing of the third mRNA nucleotide with tRNA nucleotide. The homonymy in mRNA-AA (AA for amino-acid) pairing is also present albeit rare and might be explainable in terms of context dependence of this pairing.

The article summarizes much what is known about the theoretically poorly understood role of the third nucleotide of mRNA in the translation of mRNA to AAs. That many tRNAs correspond to same mRNA - synonymy - is not surprising since the number of tRNAs is smaller than that of mRNAs. There is however also homonymy present - the third nucleotide of mRNA can correspond to several tRNAs. If the AAs associated with homonymous tRNAs are same, the is no homonymy in mRNA-AA pairing. This is not quite always the case but the deviations are surprisingly small.

The article emphasizes the fact that the codons for the standard code can be divided to two classes. For 32 codons the first two letters fix AA completely. For the remaining 32 codons there is almost unbroken symmetry in that U and C resp. A and G code for the same AA. This symmetry is broken only for the the three 4-columns of the code table containing Stop codon or Start codon coding also for met: this symmetry breaking is unavoidable given that the number of both start and Stop codons is odd. This symmetry breaking is minimal and applies only to A-G whereas T-C symmetry is exact. For the deviations of the code from the standard code the deviation as a rule breaks A-G or T-C symmetry or re-establishes it.

The notion of homonymy is extremely interesting from TGD point of view. TGD leads to two basic proposals predicting the numbers of DNA codons coding for AA rather successfully.

1. The first proposal (see this) relies on TGD view about dark matter as h_eff/h=n phases of ordinary matter motivated by adelic physics extending physics to include also the correlates of cognition (see this) . The empirical motivation comes from several sources, in particular from the findings of Pollack discussed here. One can understand the formation of negatively charged regions - exclusion zones (EZs) - as being due to the transformation of part of protons to dark protons residing at magnetic flux tubes.
   

   Dark genetic code would be realized in ters of dark proton sequences - to be denoted by DDNA, DmRNA, DtRNA, and DAA - would provide dark analogs of DNA, mRNA, tRNA, and AA. Biochemistry would emerge as a shadow of the much simpler dynamics of dark matter at flux tubes and genetic code would be induced by dark code code. The dark code would be sequence DDNA → DmRNA → DtRNA→ DAA of many-to-1 maps free of homonymies.
   
   

2. Second model of genetic code emerged accidentally from a geometric model of music harmony (see this) involving icosahedral (12 vertices-12-note scale and 20 faces-number of AAs) and tetrahedral geometries leading to the proposal that DNA codons and possibly also AAs correspond to 3-chords defining the harmony and obtained as unions of 20+20+20 3-chords associated with icosahedral 20-chord harmonies with symmetries Z₆,Z₃,Z₂ plus tetrahedral 4-chord harmony. There is large number of these harmonies bringing in additional degrees of freedom.
   

   Remark: This model has obviously analogies with the notion of wave genome introduced by Peter Gariaev.
   

   Since music both expresses and creates emotions the proposal is that these harmonies assigning additional hidden degrees of freedom to the magnetic bodies of DDNA, DRNA, etc... serve as correlates of emotions also at the molecular level. This emotional context could also give rise to context dependence of the code if several harmonies are realizable chemically. Taking seriously TGD inspired theory of consciousness (see this) and model of emotions (see this), one might say that the details of the code might depend slightly on the "emotional" state of DNA, RNA, and possibly other molecules.
   
   

In the sequel I will consider the following proposal for the various pairings of dark DNA and ordinary DNA visualizable as a 2× 4-matrix with two rows representing DDNA, DmRNA, DtRNA, DAA resp. DNA, mRNA, tRNA, AA.

1. The proposal is that genetic code at dark level extends to a sequence DDNA → DmRNA → DtRNA → DAA of horizontal pairings analogous to projections is the fundamental one, and realized via dark photon triplet resonance expect for the coupling to DAA for which coupling is based on the sum f_XYZ= f₁+f₂+f₃ of 3-chord frequencies. One might perhaps say that AA sequence defines melody and mRNA sequence the accompaniment. The frequencies f_XYZ for codons coding same AA would be same modulo octave multiple. There is context dependence and homonymies already in DmRNA-DtRNA pairing and due the fact that DtRNA corresponds to a 2-harmony as sub-harmony of 3-harmony and can be chosen in 3 different manners. Also this choice - perhaps by state function reduction - could correlate with emotional state.
   
   
2. There are also vertical mappings DDNA → DNA, DmRNA → mRNA, DtRNA → tRNA and DAA → AA. These pairings would induce the horizontal pairings DNA → mRNA → tRNA → AA at the chemical level. The homonymy at mRNA-tRNA level would have no effects on DNA-AA pairing.
   
   
3. Apart from mRNA-AA pairing all these pairings would be realized dynamically in terms of 3-chords (f₁,f₂,f₃) and giving rise to a resonant coupling between members of the pair connected by magnetic flux tubes to single dynamical unit carrying the dark photon triplets at the frequencies characterized by the 3-chord. The model for musical harmony (see this) leading also to a realization of genetic code suggests the existence of a large number of harmonies.
   

   It is not however obvious whether these harmonies can be realized bio-chemically since the 3-chords must be resonance 3-chords for bio-molecules. For DNA-AA and mRNA-AA correspondence the constraints are the slightest ones since they couple to f_XYZ= f₁+f₂+f₃: AAs could have emerged in rather early stages of the prebiotic evolution. One cannot even exclude the possibility f_XYZ are same for different harmonies. Slight chemical modifications of DNA and mRNA and AA analogous to wobbling for tRNA might allow to realize the slightly different collections of 3-chords defining the harmonies.
   
   

4. The model leads to an explanation for the homonymy of mRNA → tRNA pairing as being induced by the mRNA-tRNA homonymy realized already at dark level. The rather rare homonymies in DNA-AA pairing can be understood as accidental degeneracies. AA couples resonantly to the sum f_XYZ=f₁+f₂+f₃ of frequencies associated with codon XYZ, and one can have f_X1Y1Z1= f_X2Y2Z2 modulo octave multiple for two codons. DAA coded by DDNA codes for AA and tRNA serves only in the role of transferring DAA-AA pairs and attaching them to DmRNA-mRNA pairs: the mRNA-AA pairing would be determined completely by dark molecules. It is actually advantageous to have tRNA homonymy since it can happen that the concentration of particular certain kind of tRNA is low.
   
   
5. What distinguishes between DNA and RNA and between codons and anti-codons is not obvious in the harmonic model. The most plausible identification for the map mapping codons to anti-codons is reflection symmetry of the icosahedron permuting opposite faces. An internal reflection changing the orientation of the scale could map DNA to RNA: this makes sense if the chords can be regarded as arpeggios.
   
   
6. The vision of biological evolution as chemical evolution in which dark variants of genetic code gradually find biological representations suggests a concrete model for RNA era. At that era AAs would have catalyzed mRNA replication possibly as non-faithful process. This era might have preceded tRNA era with mRNA replaced with tRNA analog corresponding to to the fusion of two 20-chord representations. The era before this could have been era with single 20-chord representation and corresponding tRNAs and amino-acids.
   
   

See the article Homonymy of the genetic code from TGD point of view or the chapter with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.